5JII

Crystal structure of human IgG1-Fc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Fcab-HER2 Interaction: a Menage a Trois. Lessons from X-Ray and Solution Studies.

Lobner, E.Humm, A.S.Goritzer, K.Mlynek, G.Puchinger, M.G.Hasenhindl, C.Ruker, F.Traxlmayr, M.W.Djinovic-Carugo, K.Obinger, C.

(2017) Structure 25: 878-889.e5

  • DOI: https://doi.org/10.1016/j.str.2017.04.014
  • Primary Citation of Related Structures:  
    5JIH, 5JII, 5JIK, 5K33, 5KWG

  • PubMed Abstract: 

    The crystallizable fragment (Fc) of the immunoglobulin class G (IgG) is an attractive scaffold for the design of novel therapeutics. Upon engineering the C-terminal loops in the CH3 domains, Fcabs (Fc domain with antigen-binding sites) can be designed. We present the first crystal structures of Fcabs, i.e., of the HER2-binding clone H10-03-6 having the AB and EF loop engineered and the stabilized version STAB19 derived by directed evolution. Comparison with the crystal structure of the Fc wild-type protein reveals conservation of the overall domain structures but significant differences in EF-loop conformations. Furthermore, we present the first Fcab-antigen complex structures demonstrating the interaction between the engineered Fcab loops with domain IV of HER2. The crystal structures of the STAB19-HER2 and H10-03-6-HER2 complexes together with analyses by isothermal titration calorimetry, SEC-MALS, and fluorescence correlation spectroscopy show that one homodimeric Fcab binds two HER2 molecules following a negative cooperative binding behavior.


  • Organizational Affiliation

    Christian Doppler Laboratory for Antibody Engineering, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ig gamma-1 chain C region
A, B
222Homo sapiensMutation(s): 0 
Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
PHAROS:  P01857
GTEx:  ENSG00000211896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01857
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01857-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G64481DJ
GlyCosmos:  G64481DJ
GlyGen:  G64481DJ
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G61334IA
GlyCosmos:  G61334IA
GlyGen:  G61334IA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.384α = 90
b = 75.088β = 90
c = 149.403γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
XDSdata reduction
PHENIXphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Christian Doppler Research AssociationAustriaChristian Doppler Laboratory for Antibody Engineering
Austrian Science FundAustriaFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins , BioToP)

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-06-14
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary